Article
Biotechnology & Applied Microbiology
Hexin Liu, Peng Zhao, Pingfang Tian
Summary: In this study, the researchers engineered a CRISPRi system to convert glucose into glycerol and improve the production of 3-hydroxypropionic acid. The bi-functional strain with the engineered CRISPRi system showed an increase in glycerol and 3-HP production using glucose as the carbon source.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Peng Zhao, Qingyang Li, Pingfang Tian, Tianwei Tan
Summary: A newly discovered CRISPR interference system can switch glycerol metabolism pathways in Klebsiella pneumoniae, improving the production of 3-HP. Coexpressing CRISPR components and 3-HP biosynthetic enzyme significantly increased 3-HP yield, while implementing circulation feeding further improved production efficiency.
METABOLIC ENGINEERING
(2021)
Article
Agricultural Engineering
Thuan Phu Nguyen-Vo, Huichang Ryu, Michael Sauer, Sunghoon Park
Summary: The study demonstrates that deleting yieP gene in Klebsiella pneumoniae can enhance 3-HP tolerance and production, which is an effective strategy to improve microbial 3-HP production.
BIORESOURCE TECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Zhifei Chen, Hongyu Liu, Xiao Han, Ping Xu, Fei Tao
Summary: In this study, the authors successfully synthesized 1,3-propanediol (1,3-PDO) from glucose using a well-established safety strain Klebsiella oxytoca. Through a systematic metabolic engineering strategy, they were able to enhance the production of 1,3-PDO, achieving a flask fermentation titer of 6.2 g L-1. These findings have significant implications for future research on the efficient bioconversion of glucose to 1,3-PDO.
REACTION CHEMISTRY & ENGINEERING
(2023)
Article
Agricultural Engineering
Pseudomonas Asiatica, Trinh Thi Nguyen, Suman Lama, Satish Kumar Ainala, Mugesh Sankaranarayanan, Ashish Singh Chauhan, Jung Rae Kim, Sunghoon Park
Summary: The study demonstrates that Pseudomonas asiatica C1 can be a promising host for the production of 3-HP from glycerol by genetic editing and optimization, achieving high production efficiency and molar yield on glucose.
BIORESOURCE TECHNOLOGY
(2021)
Article
Polymer Science
Sai Nandhini Ravi, Mugesh Sankaranarayanan
Summary: This study aims to improve the co-production of propanediol (PDO) and 3-hydroxypropionic acid (3-HP) by isolating a new strain of K. quasipneumoniae MSN12 (KpMSN12) and overexpressing the aldH and dhaB genes. The results showed that the combined overexpression of aldH and dhaB in KpMSN12 led to higher 3-HP and PDO production, as well as improved sedimentation characteristics and increased susceptibility to antibiotics.
JOURNAL OF INORGANIC AND ORGANOMETALLIC POLYMERS AND MATERIALS
(2023)
Article
Green & Sustainable Science & Technology
Yufei Zhang, Junhua Yun, Lei Zhou, Guoyang Zhang, Mei Zhao, Hossain M. Zabed, Xianghui Qi
Summary: To achieve carbon neutrality and carbon peaking goals, sustainable biomanufacturing of high-value chemicals such as 3-hydroxypropionic acid (3-HP) through metabolic engineering of Escherichia coli has been explored. Efforts were made to optimize the biosynthetic pathway, enhance glycerol uptake, and improve the production of 3-HP through genetic engineering and process optimization. The use of corn steep liquor as a cheap fermentation medium further enhanced the production of 3-HP. Co-fermentation of crude glycerol with glucose and acetic acid resulted in high yields and productivity of 3-HP.
JOURNAL OF CLEANER PRODUCTION
(2023)
Review
Chemistry, Multidisciplinary
Fanghuan Zhu, Dehua Liu, Zhen Chen
Summary: This review provides a detailed overview of recent advancements in metabolic engineering and synthetic biology strategies for the biological production of 1,3-propanediol (1,3-PDO). It discusses the development of biological routes for 1,3-PDO production from glycerol, sugars, and other carbon sources using engineered producers, new chassis, and new pathways. The review also includes the exploration of microbial consortia and electro-fermentation processes. The challenges and future prospects of current bioproduction systems and their potential industrial applications are discussed.
Article
Biotechnology & Applied Microbiology
Shaoqi Sun, Yike Wang, Lin Shu, Xiyang Lu, Qinghui Wang, Chenguang Zhu, Jiping Shi, Gary J. Lye, Frank Baganz, Jian Hao
Summary: Klebsiella pneumoniae has been engineered to efficiently produce dihydroxyacetone and glycerol from glucose by redirecting metabolic pathways and manipulating specific genes. With the knockout of tpiA and gapA genes, overexpression of hdpA gene, disruption of dihydroxyacetone kinases, and optimization of fermentation conditions, significant improvements in product yields have been achieved. Fed batch fermentation resulted in high production levels of dihydroxyacetone and glycerol, demonstrating a novel and efficient approach to their production.
MICROBIAL CELL FACTORIES
(2021)
Article
Biotechnology & Applied Microbiology
Albert Fina, Stephanie Heux, Joan Albiol, Pau Ferrer
Summary: This study improves the productivity of Pichia pastoris in producing 3-hydroxypropionic acid by combining different metabolic engineering approaches. The results show that, in combination with using glycerol as a carbon source, the metabolically engineered strains achieved the highest concentration and productivity of 3-hydroxypropionic acid reported so far in yeast.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Shaoqi Sun, Lin Shu, Xiyang Lu, Qinghui Wang, Marina Tisma, Chenguang Zhu, Jiping Shi, Frank Baganz, Gary J. Lye, Jian Hao
Summary: The study demonstrates an efficient way of producing 1,2-propanediol from glycerol via an endogenous pathway of K. pneumoniae. Key enzymes for 1,2-propanediol synthesis were identified, and optimal process parameters were determined for maximal production in the strain.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Agricultural Engineering
Yufei Zhang, Junhua Yun, Hossain M. Zabed, Yuan Dou, Guoyan Zhang, Mei Zhao, Mohammad J. Taherzadeh, Arthur Ragauskas, Xianghui Qi
Summary: This study improves the co-production of 3-hydroxypropionic acid (3-HP) and 1,3-propanediol (1,3-PDO) by metabolic engineering of Escherichia coli and process optimization. The co-biosynthetic pathways of 3-HP and 1,3-PDO were recruited and optimized in E. coli, coupled with cofactor regeneration systems to increase product synthesis. Pathway rebalancing and block of by-product formation improved the net titer of 3-HP and 1,3-PDO. Glycerol flux towards 3-HP and 1,3-PDO synthesis was maximized by removing metabolic repression and fine-tuning the glycerol oxidation pathway. The optimized fermentation process produced 140.50 g/L of 3-HP and 1,3-PDO, with a net yield of 0.85 mol/mol.
BIORESOURCE TECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Di Liu, Hee Jin Hwang, Peter B. Otoupal, Gina M. Geiselman, Joonhoon Kim, Kyle R. Pomraning, Young-Mo Kim, Nathalie Munoz, Carrie D. Nicora, Yuqian Gao, Kristin E. Burnum-Johnson, Oslo Jacobson, Samuel Coradetti, Jinho Kim, Shuang Deng, Ziyu Dai, Jan-Philip Prahl, Deepti Tanjore, Taek Soon Lee, Jon K. Magnuson, John M. Gladden
Summary: Microbial production of valuable bioproducts is an important strategy for sustainable manufacturing. In this study, the oleaginous yeast, Rhodosporidium toruloides, was engineered to produce 3-hydroxypropionic acid (3HP) from lignocellulosic hydrolysates. The researchers used functional genomics and metabolomic analysis to identify catabolic pathways, and discovered a novel 3HP transporter in Aspergillus pseudoterreus. Through engineering efforts and media optimization, they achieved a high 3HP titer of 45.4 g/L. This work establishes R. toruloides as a promising host for 3HP production from lignocellulosic feedstocks.
METABOLIC ENGINEERING
(2023)
Review
Biotechnology & Applied Microbiology
Peng Zhao, Pingfang Tian
Summary: This review summarizes key factors in bacterial production of 3-HP, including host strains, metabolic pathways, key enzymes, and challenges in achieving high yields.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Shimin Wu, Peng Zhao, Qingyang Li, Pingfang Tian
Summary: Intensifying niacin-based biosynthesis of NAD(+) significantly enhances 3-hydroxypropionic acid production in Klebsiella pneumoniae. Overexpressing nicotinate phosphoribosyltransferase (PncB) in the strain increases NAD(+) production, leading to improved 3-HP production. Further optimization by coexpressing PncB with PuuC and supplementing niacin in shake flask and bioreactor resulted in even higher yields of 3-HP.
BIOTECHNOLOGY LETTERS
(2021)
Article
Multidisciplinary Sciences
Ying Li, Jinqing Wei, Huizhen Yang, Jing Dai, Xizhen Ge
Summary: Berberine partially inhibits the enzyme activities of cutinase from fungal pathogen C. capsici, leading to decreased rigidity of the enzyme. Molecular dynamics simulation suggests that berberine aggregates at the catalytic center of cutinase, resulting in stronger hydrophobic interactions and conformational changes in key residues.
Article
Plant Sciences
Ying Li, Honglin Wen, Xizhen Ge
Summary: The study found that low concentrations of berberine can accelerate the growth of bacterial pathogens such as Klebsiella pneumoniae through hormesis, while higher concentrations have the opposite effect. The mechanisms of action of this drug at low concentrations are still poorly understood.
JOURNAL OF NATURAL PRODUCTS
(2021)
Article
Biochemistry & Molecular Biology
Huizhen Yang, Runying He, Yao Cui, Ying Li, Xizhen Ge
Summary: This article reveals that the degradation of cellulose in Agarwood by saprophytic Bacillus subtilis is the driving force behind the release of its effective components. The study provides a promising approach to accelerate the release of effective components in Agarwood using bacterial agents.
Article
Microbiology
Ying Li, Trevor S. Cross, Tobias Dorr
Summary: Infections caused by Klebsiella pneumoniae are difficult to manage due to high rates of multidrug resistance, often caused by efflux pumps. This study analyzed the sequence variations of the AcrB efflux pump from K. pneumoniae genomes and found prevalent variants in clinical isolates. Molecular dynamics analysis revealed conformational changes in two variants that may enhance drug efflux capabilities. Experimental results showed that these variants had slightly increased growth and survival abilities in the presence of specific antibiotics. The emergence of these enhanced-function AcrB variants may pose a potential risk for increased antibiotic resistance in clinical K. pneumoniae isolates.
RESEARCH IN MICROBIOLOGY
(2022)
Article
Horticulture
Geran Tian, Ying Li
Summary: By using lignocellulose mulch, soil properties can be improved, weed growth and diseases can be suppressed, and the yield and quality of Chinese chestnuts can be increased, showing a significant cost-benefit advantage.
SCIENTIA HORTICULTURAE
(2022)
Article
Immunology
Ying Li, Honglin Wen, Xizhen Ge
Summary: This study analyzed the effect of different variants of the efflux pump KmrA on its export efficiency. The researchers found that the opposite motion of the pump's central helices is important for its function, and provided detailed information on the molecular dynamics and conformational changes involved.
MICROBIAL PATHOGENESIS
(2022)
Article
Biochemistry & Molecular Biology
Ying Li, Runying He, Xizhen Ge
Summary: This study demonstrated that activation of dha regulon in Klebsiella pneumoniae efficiently promotes biomass accumulation. Transcriptome analysis revealed that the regulator was activated by the supply of glycerol, leading to increased biomass without affecting antibiotic susceptibility.
PROCESS BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Ying Li, Xizhen Ge
Summary: The study investigated the natural mutations of the KmrA gene in Klebsiella pneumoniae and identified two variants that enhanced multidrug resistance. Through molecular dynamics simulations, it was revealed that these mutations increased drug export efficiency by strengthening the interactions between KmrA and water as well as the cell membrane, and promoting conformational changes.
Article
Biochemistry & Molecular Biology
Runying He, Yao Cui, Ying Li, Xizhen Ge
Summary: This study investigated the degradation of berberine in soil water and its impact on bacterial diversity. The results showed that berberine only degraded in soil water, while remaining stable in tap water, river water, and aquaculture water. The study also identified the essential role of the bacterial genus Methylotenera in berberine degradation.
Article
Biochemistry & Molecular Biology
Ying Li, Xizhen Ge
Summary: Multidrug resistance is a challenge to antibiotic therapy, mainly caused by efflux pumps in bacterial membranes. MFS efflux pumps are associated with quinolone resistance. This study used MdfA as a representative MFS efflux pump to investigate its conformational transition. Molecular dynamics simulations revealed an intermediate state between the inward and outward conformations, with protonation initiating the transition from outward to inward. Hydrophilic interaction and structural changes favored this process, while hydrophobic interaction and altered salt bridges facilitated substrate entrance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Ying Li, Xizhen Ge
Summary: This study investigates the impact of internal ionic interactions on the antibiotic resistance of E. coli by studying a representative MFS efflux pump called MdfA. The researchers found that extending the salt bridge on the cytoplasmic side of MdfA resulted in elevated antibiotic resistance, which was further enhanced by combining it with an artificial mutation. By analyzing molecular dynamics simulations, they discovered that enhanced interactions led to a larger surface for MdfA's protonation, indicating a higher possibility for its activation.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Microbiology
Ying Li, Xizhen Ge
Summary: In this work, we evaluated the role of berberine (BBR) as an inhibitor of the MFS efflux pump MdfA from E. coli. We demonstrated that low levels of BBR significantly increased intracellular ciprofloxacin concentrations and restored antibiotic susceptibility of the reporter strain. Molecular dynamics simulations revealed the effect of BBR on the conformational transition of MdfA. Our data suggested that driving forces for MdfA's conformational transition were affected by BBR and provided evidence for BBR's extended application as an effective inhibitor of MdfA.
MICROBIOLOGY SPECTRUM
(2023)
Article
Nanoscience & Nanotechnology
Ying Li, Runying He, Yao Cui, Xizhen Ge
Summary: The study reveals that berberine (BBR) forms clusters in water and sodium stearate (ST), as a dispersant, can weaken the hydrophobic strength of BBR clusters. When BBR is combined with ST, it enhances the hydrophobic interactions between BBR and the catalytic center of cutinase, leading to the inactivation of cutinase. Wet experiments confirm the synergistic effect of BBR and ST in reducing cutinase activity.
ACS APPLIED BIO MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Ying Li, Zheng Liu, Xizhen Ge
Summary: The study demonstrated a forward beta-oxidation pathway for 1-BD production from kitchen waste oil in Pseudomonas aeruginosa, with ALDH being identified as a crucial factor in diverting metabolic flux into 1-BD biosynthesis. Deletion of ALDH8 and ALDH9 resulted in a significant decrease in 1-BD titers, while overexpression of these ALDHs led to an increase in 1-BD production.
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2021)
Article
Agricultural Engineering
Ying Li, Miaomiao Chi, Xizhen Ge
INTERNATIONAL JOURNAL OF AGRICULTURAL AND BIOLOGICAL ENGINEERING
(2019)
